Abstract
River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.
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Acknowledgements
The authors acknowledge the State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University for research support. The authors also acknowledge the Resource and Environmental Science Data Platform (https://www.resdc.cn/) and WorldClim database (https://www.worldclim.org/) for providing geographic data. The authors thank Majorbio Company (Shanghai, China) for technical support and the High-performance Computing Platform of Peking University for providing computational resources.
Funding
J.R.N. and Q.C. discloses support for the research of this work from the National Natural Science Foundation of China [grant number U2240205].
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Deng, C., Cai, H., Luo, K. et al. Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-74161-2
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DOI: https://doi.org/10.1038/s41467-026-74161-2
Source: Ecology - nature.com
